Multiple sequence alignment - TraesCS2B01G433800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G433800 chr2B 100.000 4550 0 0 1 4550 622918435 622913886 0.000000e+00 8403.0
1 TraesCS2B01G433800 chr2A 93.123 4115 206 41 215 4299 671708209 671704142 0.000000e+00 5960.0
2 TraesCS2B01G433800 chr2A 93.103 174 12 0 4377 4550 671704029 671703856 5.840000e-64 255.0
3 TraesCS2B01G433800 chr2A 89.062 128 12 1 86 213 671708427 671708302 1.690000e-34 158.0
4 TraesCS2B01G433800 chr2A 87.324 71 2 3 1 64 671708496 671708426 1.760000e-09 75.0
5 TraesCS2B01G433800 chr2D 93.952 2811 130 19 772 3570 526519735 526516953 0.000000e+00 4213.0
6 TraesCS2B01G433800 chr2D 94.628 726 35 3 3609 4332 526516951 526516228 0.000000e+00 1122.0
7 TraesCS2B01G433800 chr2D 88.367 980 49 26 1827 2795 274923326 274924251 0.000000e+00 1118.0
8 TraesCS2B01G433800 chr2D 93.011 744 37 7 41 771 526520796 526520055 0.000000e+00 1072.0
9 TraesCS2B01G433800 chr2D 94.828 174 9 0 4377 4550 526516230 526516057 5.800000e-69 272.0
10 TraesCS2B01G433800 chr6B 89.173 979 51 23 1827 2795 27634227 27633294 0.000000e+00 1170.0
11 TraesCS2B01G433800 chr6B 89.899 99 6 1 4329 4423 530560464 530560366 1.720000e-24 124.0
12 TraesCS2B01G433800 chr6B 83.871 93 15 0 3998 4090 496988445 496988537 6.270000e-14 89.8
13 TraesCS2B01G433800 chr4D 89.082 980 42 28 1827 2795 455258961 455258036 0.000000e+00 1157.0
14 TraesCS2B01G433800 chr7B 88.360 988 50 28 1827 2795 145929508 145928567 0.000000e+00 1127.0
15 TraesCS2B01G433800 chr7B 91.901 605 27 5 2195 2795 4604456 4605042 0.000000e+00 826.0
16 TraesCS2B01G433800 chr5B 88.367 980 58 23 1827 2795 504043727 504044661 0.000000e+00 1127.0
17 TraesCS2B01G433800 chr6D 90.036 823 38 23 1827 2641 97558766 97559552 0.000000e+00 1026.0
18 TraesCS2B01G433800 chr6D 90.816 98 6 3 4328 4422 324520677 324520774 1.330000e-25 128.0
19 TraesCS2B01G433800 chr6D 83.871 93 15 0 3998 4090 325819719 325819627 6.270000e-14 89.8
20 TraesCS2B01G433800 chr3B 87.457 582 41 18 1827 2402 85095477 85094922 3.840000e-180 641.0
21 TraesCS2B01G433800 chr3B 87.415 294 15 5 2506 2795 85094710 85094435 7.350000e-83 318.0
22 TraesCS2B01G433800 chr3B 78.903 474 51 15 2837 3286 586050825 586051273 4.480000e-70 276.0
23 TraesCS2B01G433800 chr3B 90.055 181 15 2 3374 3554 586051338 586051515 9.840000e-57 231.0
24 TraesCS2B01G433800 chr3B 89.051 137 15 0 4226 4362 586130245 586130381 2.180000e-38 171.0
25 TraesCS2B01G433800 chr3B 93.407 91 6 0 4130 4220 586051517 586051607 7.940000e-28 135.0
26 TraesCS2B01G433800 chr3B 86.869 99 9 3 4331 4425 685063123 685063025 1.730000e-19 108.0
27 TraesCS2B01G433800 chr3B 81.522 92 11 4 4331 4417 370162506 370162596 2.270000e-08 71.3
28 TraesCS2B01G433800 chr7A 89.899 99 6 1 4331 4425 85209302 85209400 1.720000e-24 124.0
29 TraesCS2B01G433800 chr7A 86.408 103 11 3 4323 4423 159698738 159698839 4.810000e-20 110.0
30 TraesCS2B01G433800 chr6A 87.255 102 8 3 4330 4427 34179548 34179648 1.340000e-20 111.0
31 TraesCS2B01G433800 chr6A 83.871 93 15 0 3998 4090 464689285 464689193 6.270000e-14 89.8
32 TraesCS2B01G433800 chr3D 85.185 108 16 0 4330 4437 406158328 406158435 1.340000e-20 111.0
33 TraesCS2B01G433800 chr1D 87.500 96 8 3 4332 4423 47710798 47710703 1.730000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G433800 chr2B 622913886 622918435 4549 True 8403.00 8403 100.00000 1 4550 1 chr2B.!!$R1 4549
1 TraesCS2B01G433800 chr2A 671703856 671708496 4640 True 1612.00 5960 90.65300 1 4550 4 chr2A.!!$R1 4549
2 TraesCS2B01G433800 chr2D 526516057 526520796 4739 True 1669.75 4213 94.10475 41 4550 4 chr2D.!!$R1 4509
3 TraesCS2B01G433800 chr2D 274923326 274924251 925 False 1118.00 1118 88.36700 1827 2795 1 chr2D.!!$F1 968
4 TraesCS2B01G433800 chr6B 27633294 27634227 933 True 1170.00 1170 89.17300 1827 2795 1 chr6B.!!$R1 968
5 TraesCS2B01G433800 chr4D 455258036 455258961 925 True 1157.00 1157 89.08200 1827 2795 1 chr4D.!!$R1 968
6 TraesCS2B01G433800 chr7B 145928567 145929508 941 True 1127.00 1127 88.36000 1827 2795 1 chr7B.!!$R1 968
7 TraesCS2B01G433800 chr7B 4604456 4605042 586 False 826.00 826 91.90100 2195 2795 1 chr7B.!!$F1 600
8 TraesCS2B01G433800 chr5B 504043727 504044661 934 False 1127.00 1127 88.36700 1827 2795 1 chr5B.!!$F1 968
9 TraesCS2B01G433800 chr6D 97558766 97559552 786 False 1026.00 1026 90.03600 1827 2641 1 chr6D.!!$F1 814
10 TraesCS2B01G433800 chr3B 85094435 85095477 1042 True 479.50 641 87.43600 1827 2795 2 chr3B.!!$R2 968
11 TraesCS2B01G433800 chr3B 586050825 586051607 782 False 214.00 276 87.45500 2837 4220 3 chr3B.!!$F3 1383

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
445 545 0.872021 GCCAATACGCTCGAGACAGG 60.872 60.0 18.75 9.32 0.0 4.00 F
2134 2591 0.193574 ACCTCTCCCCTTCAGACCAA 59.806 55.0 0.00 0.00 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2616 0.032952 TTACACCGGTGAGTGAGTGC 59.967 55.0 40.21 0.0 40.34 4.40 R
3987 4612 0.031585 TCGTCGACTTCACACTTGGG 59.968 55.0 14.70 0.0 0.00 4.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.310224 GCATCGTTTACCAGCATTGTTTATTT 59.690 34.615 0.00 0.00 0.00 1.40
35 36 7.148656 GCATCGTTTACCAGCATTGTTTATTTT 60.149 33.333 0.00 0.00 0.00 1.82
64 72 5.914898 AGGGTATTGTTTATTGCCTGTTC 57.085 39.130 0.00 0.00 0.00 3.18
110 119 2.970640 AGTCTTTGTTACCTTCCGACCT 59.029 45.455 0.00 0.00 0.00 3.85
122 131 2.027625 CCGACCTGTGGAGCGTTTC 61.028 63.158 0.00 0.00 0.00 2.78
187 196 1.466167 CATTTTGGTCAGTCGAGGCAG 59.534 52.381 0.00 0.00 0.00 4.85
201 210 3.071312 TCGAGGCAGGTGGTAAAGTTTTA 59.929 43.478 0.00 0.00 0.00 1.52
273 373 1.574428 GTCGTTCGGTGCTGCAATT 59.426 52.632 2.77 0.00 0.00 2.32
294 394 3.753815 TCCATCAGATTTGCACTTGTCA 58.246 40.909 0.00 0.00 0.00 3.58
342 442 7.396540 AATTAAACTTGGGTCTAAGCATCTG 57.603 36.000 0.00 0.00 0.00 2.90
346 446 3.274288 CTTGGGTCTAAGCATCTGTTCC 58.726 50.000 0.00 0.00 0.00 3.62
445 545 0.872021 GCCAATACGCTCGAGACAGG 60.872 60.000 18.75 9.32 0.00 4.00
447 547 1.268794 CCAATACGCTCGAGACAGGAG 60.269 57.143 18.75 0.79 34.62 3.69
451 551 1.451567 CGCTCGAGACAGGAGGGTA 60.452 63.158 18.75 0.00 39.02 3.69
476 576 1.488393 GGACTGGATCTTAAGCAGCCT 59.512 52.381 8.10 0.00 0.00 4.58
518 618 4.024048 CAGCGAGTGGTTCTTTGTTTATGT 60.024 41.667 0.00 0.00 0.00 2.29
595 708 4.393062 GTCAGTACTGTGATGTTCCAATGG 59.607 45.833 21.99 0.00 0.00 3.16
637 750 1.855360 GGCAAATTTGTTCGACGCAAA 59.145 42.857 19.03 14.25 39.69 3.68
743 857 1.134965 CCAAAACGCCTCACAAAACCA 60.135 47.619 0.00 0.00 0.00 3.67
762 876 3.825160 TTGGCGCTCGCTCCAAACT 62.825 57.895 10.64 0.00 37.79 2.66
763 877 3.491652 GGCGCTCGCTCCAAACTC 61.492 66.667 7.64 0.00 41.60 3.01
828 1261 4.937620 CGATTCTTCCCATCAAGAAAGTGA 59.062 41.667 0.01 0.00 43.88 3.41
833 1266 2.005451 CCCATCAAGAAAGTGAGCTCG 58.995 52.381 9.64 0.00 0.00 5.03
871 1304 9.907576 CATATTAGACGAGACAAAAATGAAGTC 57.092 33.333 0.00 0.00 0.00 3.01
928 1361 1.373748 GTTGCGGAAGTACCAGCGA 60.374 57.895 0.00 0.00 39.62 4.93
973 1406 2.884639 CCACAAGGAACCAAGTAACCAG 59.115 50.000 0.00 0.00 36.89 4.00
1058 1491 3.782443 CCACGGCTACCACCCTCC 61.782 72.222 0.00 0.00 0.00 4.30
1059 1492 2.683933 CACGGCTACCACCCTCCT 60.684 66.667 0.00 0.00 0.00 3.69
1067 1500 3.775654 CCACCCTCCTCTCCACGC 61.776 72.222 0.00 0.00 0.00 5.34
1191 1624 0.471211 ACAACCTCCTCTTCCGGTCA 60.471 55.000 0.00 0.00 0.00 4.02
1368 1801 2.203938 TCCTTCCGCTTCCACCCT 60.204 61.111 0.00 0.00 0.00 4.34
1453 1890 4.193334 GAGGGAATTTGGCGGCGC 62.193 66.667 26.17 26.17 0.00 6.53
1492 1934 2.762745 GATCGCGGTGTGGGTTTATAT 58.237 47.619 6.13 0.00 0.00 0.86
1499 1941 3.738899 CGGTGTGGGTTTATATAGCACGT 60.739 47.826 0.00 0.00 0.00 4.49
1759 2201 3.436924 TTCGACCTGCTCGCGCTA 61.437 61.111 5.56 0.00 42.62 4.26
1911 2355 7.952671 TGTTCACTTTGAGACATAGACTAGTT 58.047 34.615 0.00 0.00 0.00 2.24
2086 2543 4.899239 GACATGCTCCTCCCGCGG 62.899 72.222 21.04 21.04 0.00 6.46
2118 2575 1.185618 TTCTACGGTCTGCAGCACCT 61.186 55.000 23.96 16.61 0.00 4.00
2120 2577 1.599606 CTACGGTCTGCAGCACCTCT 61.600 60.000 23.96 15.39 0.00 3.69
2121 2578 1.595993 TACGGTCTGCAGCACCTCTC 61.596 60.000 23.96 6.87 0.00 3.20
2123 2580 2.267324 GTCTGCAGCACCTCTCCC 59.733 66.667 9.47 0.00 0.00 4.30
2124 2581 3.005539 TCTGCAGCACCTCTCCCC 61.006 66.667 9.47 0.00 0.00 4.81
2125 2582 3.007920 CTGCAGCACCTCTCCCCT 61.008 66.667 0.00 0.00 0.00 4.79
2126 2583 2.530151 TGCAGCACCTCTCCCCTT 60.530 61.111 0.00 0.00 0.00 3.95
2127 2584 2.270527 GCAGCACCTCTCCCCTTC 59.729 66.667 0.00 0.00 0.00 3.46
2128 2585 2.596851 GCAGCACCTCTCCCCTTCA 61.597 63.158 0.00 0.00 0.00 3.02
2129 2586 1.601171 CAGCACCTCTCCCCTTCAG 59.399 63.158 0.00 0.00 0.00 3.02
2130 2587 0.906756 CAGCACCTCTCCCCTTCAGA 60.907 60.000 0.00 0.00 0.00 3.27
2134 2591 0.193574 ACCTCTCCCCTTCAGACCAA 59.806 55.000 0.00 0.00 0.00 3.67
2135 2592 1.362224 CCTCTCCCCTTCAGACCAAA 58.638 55.000 0.00 0.00 0.00 3.28
2136 2593 1.918957 CCTCTCCCCTTCAGACCAAAT 59.081 52.381 0.00 0.00 0.00 2.32
2137 2594 2.092699 CCTCTCCCCTTCAGACCAAATC 60.093 54.545 0.00 0.00 0.00 2.17
2138 2595 1.555075 TCTCCCCTTCAGACCAAATCG 59.445 52.381 0.00 0.00 0.00 3.34
2139 2596 0.618458 TCCCCTTCAGACCAAATCGG 59.382 55.000 0.00 0.00 42.50 4.18
2149 2606 2.159181 CCAAATCGGTGTCGTCCAC 58.841 57.895 0.25 0.25 43.74 4.02
2156 2613 2.259511 GTGTCGTCCACCGTACCC 59.740 66.667 0.00 0.00 38.18 3.69
2157 2614 2.203466 TGTCGTCCACCGTACCCA 60.203 61.111 0.00 0.00 37.94 4.51
2158 2615 2.259511 GTCGTCCACCGTACCCAC 59.740 66.667 0.00 0.00 37.94 4.61
2167 2624 2.649034 CGTACCCACGCACTCACT 59.351 61.111 0.00 0.00 42.05 3.41
2168 2625 1.443872 CGTACCCACGCACTCACTC 60.444 63.158 0.00 0.00 42.05 3.51
2169 2626 1.663739 GTACCCACGCACTCACTCA 59.336 57.895 0.00 0.00 0.00 3.41
2170 2627 0.666577 GTACCCACGCACTCACTCAC 60.667 60.000 0.00 0.00 0.00 3.51
2171 2628 1.812686 TACCCACGCACTCACTCACC 61.813 60.000 0.00 0.00 0.00 4.02
2172 2629 2.734723 CCACGCACTCACTCACCG 60.735 66.667 0.00 0.00 0.00 4.94
2173 2630 2.734723 CACGCACTCACTCACCGG 60.735 66.667 0.00 0.00 0.00 5.28
2174 2631 3.224324 ACGCACTCACTCACCGGT 61.224 61.111 0.00 0.00 0.00 5.28
2175 2632 2.734723 CGCACTCACTCACCGGTG 60.735 66.667 29.26 29.26 38.44 4.94
2176 2633 2.421739 GCACTCACTCACCGGTGT 59.578 61.111 32.74 13.54 38.28 4.16
2177 2634 1.663739 GCACTCACTCACCGGTGTA 59.336 57.895 32.74 18.79 38.28 2.90
2178 2635 0.032952 GCACTCACTCACCGGTGTAA 59.967 55.000 32.74 15.11 38.28 2.41
2179 2636 1.779569 CACTCACTCACCGGTGTAAC 58.220 55.000 32.74 0.00 38.28 2.50
2180 2637 1.340248 CACTCACTCACCGGTGTAACT 59.660 52.381 32.74 11.85 38.28 2.24
2191 2648 1.732259 CGGTGTAACTTCACTGATGGC 59.268 52.381 0.01 0.00 44.64 4.40
2228 2689 2.039405 GCTTCAGGCTGGTGCAGAG 61.039 63.158 15.73 4.85 41.91 3.35
2241 2702 2.182030 CAGAGGCGGGAGTTCGTC 59.818 66.667 0.00 0.00 34.63 4.20
2352 2821 4.511246 ATGCTGGCCATGACGGGG 62.511 66.667 5.51 0.00 31.48 5.73
2651 3229 3.599730 TCAGTTGATCTTCGTCTGCAT 57.400 42.857 0.00 0.00 0.00 3.96
2769 3358 0.322546 ACCCTTCCTTCATGAACGCC 60.323 55.000 3.38 0.00 0.00 5.68
2827 3416 3.668656 GGTGAACGAATGCTTGTTTTAGC 59.331 43.478 0.00 0.00 41.59 3.09
2867 3458 3.963665 TGTCAAATTTCAGCAGGTTTCG 58.036 40.909 0.00 0.00 0.00 3.46
2915 3506 2.325583 TGTTCGGGCCTATGACAATC 57.674 50.000 0.84 0.00 0.00 2.67
3098 3712 2.994186 ATAGGTTCATTTACGCGGGT 57.006 45.000 12.47 10.91 0.00 5.28
3146 3760 4.658063 TCCCATATTTTCCGTTTGACAGT 58.342 39.130 0.00 0.00 0.00 3.55
3302 3922 8.090788 AGGTAAATACATATGTCCTGTCAGTT 57.909 34.615 12.68 1.81 0.00 3.16
3303 3923 8.204836 AGGTAAATACATATGTCCTGTCAGTTC 58.795 37.037 12.68 0.00 0.00 3.01
3319 3939 7.118390 CCTGTCAGTTCATACAAAACTCTTAGG 59.882 40.741 0.00 0.00 34.79 2.69
3359 3979 5.418840 TCAATAACTTCCAAAGATTCCAGGC 59.581 40.000 0.00 0.00 0.00 4.85
3372 3992 1.974265 TCCAGGCGTTTCAAACATCA 58.026 45.000 0.22 0.00 0.00 3.07
3566 4186 1.712401 TGAATGGCAAAAATCGCAGC 58.288 45.000 0.00 0.00 0.00 5.25
3571 4191 2.088178 GCAAAAATCGCAGCCACCG 61.088 57.895 0.00 0.00 0.00 4.94
3579 4199 2.343758 GCAGCCACCGACTCTGAA 59.656 61.111 0.00 0.00 0.00 3.02
3590 4210 3.251004 ACCGACTCTGAAAAGCAATTGTC 59.749 43.478 7.40 0.00 0.00 3.18
3597 4217 2.297033 TGAAAAGCAATTGTCAGGCTCC 59.703 45.455 7.40 0.00 36.76 4.70
3643 4263 8.827177 ATCGATTTTGATAGGAGCGTAAAATA 57.173 30.769 0.00 0.00 32.79 1.40
3699 4319 5.349270 TCCGTTCTTATACAACAACCATTCG 59.651 40.000 0.00 0.00 0.00 3.34
3710 4331 1.398390 CAACCATTCGTAGGAGCTTGC 59.602 52.381 0.00 0.00 0.00 4.01
3711 4332 0.460284 ACCATTCGTAGGAGCTTGCG 60.460 55.000 0.00 0.00 0.00 4.85
3777 4401 3.011818 CAGCAGGATAACAAGCATGACA 58.988 45.455 0.00 0.00 0.00 3.58
3880 4505 1.301423 TGTAACACCACGGCAACTTC 58.699 50.000 0.00 0.00 0.00 3.01
3894 4519 5.168569 CGGCAACTTCTAATGTTCTAGACA 58.831 41.667 0.00 0.00 43.71 3.41
3935 4560 3.941483 CTGTCCCTGATCACAACCATAAC 59.059 47.826 0.00 0.00 0.00 1.89
3943 4568 4.895889 TGATCACAACCATAACAAACCCAA 59.104 37.500 0.00 0.00 0.00 4.12
3987 4612 6.481434 ACTGATCCTGTACAATACTAACCC 57.519 41.667 0.00 0.00 0.00 4.11
4095 4720 5.242069 ACATTCTCACTACATCGTCAGAG 57.758 43.478 0.00 0.00 0.00 3.35
4266 4891 8.666573 GTTTCCTTAGCTGAAAAGTAGGATAAC 58.333 37.037 0.00 0.00 33.80 1.89
4273 4898 6.660949 AGCTGAAAAGTAGGATAACTTGCATT 59.339 34.615 0.00 0.00 39.62 3.56
4276 4901 8.506168 TGAAAAGTAGGATAACTTGCATTAGG 57.494 34.615 0.00 0.00 39.62 2.69
4302 5009 6.272090 TGCAGATCCACCCAACATAATAGATA 59.728 38.462 0.00 0.00 0.00 1.98
4312 5019 7.709613 ACCCAACATAATAGATACGACTTTGAC 59.290 37.037 0.00 0.00 0.00 3.18
4332 5039 5.413499 TGACGGAACAGCTAAATAAGGTAC 58.587 41.667 0.00 0.00 33.59 3.34
4334 5041 5.658468 ACGGAACAGCTAAATAAGGTACTC 58.342 41.667 0.00 0.00 38.49 2.59
4335 5042 5.048507 CGGAACAGCTAAATAAGGTACTCC 58.951 45.833 0.00 0.00 38.49 3.85
4336 5043 5.366460 GGAACAGCTAAATAAGGTACTCCC 58.634 45.833 0.00 0.00 38.49 4.30
4338 5045 5.873146 ACAGCTAAATAAGGTACTCCCTC 57.127 43.478 0.00 0.00 45.47 4.30
4339 5046 4.654724 ACAGCTAAATAAGGTACTCCCTCC 59.345 45.833 0.00 0.00 45.47 4.30
4340 5047 3.896272 AGCTAAATAAGGTACTCCCTCCG 59.104 47.826 0.00 0.00 45.47 4.63
4341 5048 3.893813 GCTAAATAAGGTACTCCCTCCGA 59.106 47.826 0.00 0.00 45.47 4.55
4342 5049 4.527427 GCTAAATAAGGTACTCCCTCCGAT 59.473 45.833 0.00 0.00 45.47 4.18
4343 5050 5.336610 GCTAAATAAGGTACTCCCTCCGATC 60.337 48.000 0.00 0.00 45.47 3.69
4344 5051 2.671896 TAAGGTACTCCCTCCGATCC 57.328 55.000 0.00 0.00 45.47 3.36
4345 5052 0.635009 AAGGTACTCCCTCCGATCCA 59.365 55.000 0.00 0.00 45.47 3.41
4346 5053 0.861155 AGGTACTCCCTCCGATCCAT 59.139 55.000 0.00 0.00 40.71 3.41
4347 5054 2.071372 AGGTACTCCCTCCGATCCATA 58.929 52.381 0.00 0.00 40.71 2.74
4348 5055 2.655407 AGGTACTCCCTCCGATCCATAT 59.345 50.000 0.00 0.00 40.71 1.78
4349 5056 3.077695 AGGTACTCCCTCCGATCCATATT 59.922 47.826 0.00 0.00 40.71 1.28
4350 5057 4.294168 AGGTACTCCCTCCGATCCATATTA 59.706 45.833 0.00 0.00 40.71 0.98
4351 5058 5.021458 GGTACTCCCTCCGATCCATATTAA 58.979 45.833 0.00 0.00 0.00 1.40
4352 5059 5.661759 GGTACTCCCTCCGATCCATATTAAT 59.338 44.000 0.00 0.00 0.00 1.40
4353 5060 6.156429 GGTACTCCCTCCGATCCATATTAATT 59.844 42.308 0.00 0.00 0.00 1.40
4354 5061 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
4355 5062 5.548056 ACTCCCTCCGATCCATATTAATTGT 59.452 40.000 0.00 0.00 0.00 2.71
4356 5063 6.049955 TCCCTCCGATCCATATTAATTGTC 57.950 41.667 0.00 0.00 0.00 3.18
4357 5064 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
4358 5065 4.330074 CCTCCGATCCATATTAATTGTCGC 59.670 45.833 0.00 0.00 0.00 5.19
4359 5066 5.147330 TCCGATCCATATTAATTGTCGCT 57.853 39.130 0.00 0.00 0.00 4.93
4360 5067 4.929211 TCCGATCCATATTAATTGTCGCTG 59.071 41.667 0.00 0.00 0.00 5.18
4361 5068 4.929211 CCGATCCATATTAATTGTCGCTGA 59.071 41.667 0.00 0.00 0.00 4.26
4362 5069 5.582269 CCGATCCATATTAATTGTCGCTGAT 59.418 40.000 0.00 0.00 0.00 2.90
4363 5070 6.092670 CCGATCCATATTAATTGTCGCTGATT 59.907 38.462 0.00 0.00 0.00 2.57
4364 5071 7.361201 CCGATCCATATTAATTGTCGCTGATTT 60.361 37.037 0.00 0.00 0.00 2.17
4365 5072 8.655970 CGATCCATATTAATTGTCGCTGATTTA 58.344 33.333 0.00 0.00 0.00 1.40
4366 5073 9.979270 GATCCATATTAATTGTCGCTGATTTAG 57.021 33.333 0.00 0.00 0.00 1.85
4367 5074 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
4368 5075 9.990360 TCCATATTAATTGTCGCTGATTTAGTA 57.010 29.630 0.00 0.00 0.00 1.82
4373 5080 8.542497 TTAATTGTCGCTGATTTAGTACAACT 57.458 30.769 0.00 0.00 37.29 3.16
4374 5081 7.435068 AATTGTCGCTGATTTAGTACAACTT 57.565 32.000 0.00 0.00 37.29 2.66
4375 5082 6.854496 TTGTCGCTGATTTAGTACAACTTT 57.146 33.333 0.00 0.00 32.84 2.66
4376 5083 6.223138 TGTCGCTGATTTAGTACAACTTTG 57.777 37.500 0.00 0.00 0.00 2.77
4377 5084 5.756347 TGTCGCTGATTTAGTACAACTTTGT 59.244 36.000 0.00 0.00 44.86 2.83
4378 5085 6.924612 TGTCGCTGATTTAGTACAACTTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
4397 5104 8.780249 ACTTTGTAATTTGTACTAAATCAGCGT 58.220 29.630 0.00 0.00 0.00 5.07
4424 5131 4.405756 AATATGGATCGGAGGGAGTACT 57.594 45.455 0.00 0.00 0.00 2.73
4431 5138 2.168496 TCGGAGGGAGTACTGAAGTTG 58.832 52.381 0.00 0.00 0.00 3.16
4437 5144 6.342111 GGAGGGAGTACTGAAGTTGATAAAG 58.658 44.000 0.00 0.00 0.00 1.85
4445 5152 6.300354 ACTGAAGTTGATAAAGTTTGACGG 57.700 37.500 0.00 0.00 0.00 4.79
4446 5153 5.103290 TGAAGTTGATAAAGTTTGACGGC 57.897 39.130 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.295357 CTGGTAAACGATGCACGCCA 61.295 55.000 8.31 6.97 46.94 5.69
34 35 7.233757 AGGCAATAAACAATACCCTAAACACAA 59.766 33.333 0.00 0.00 0.00 3.33
35 36 6.722129 AGGCAATAAACAATACCCTAAACACA 59.278 34.615 0.00 0.00 0.00 3.72
64 72 0.170339 TGGTCGACGCATGACACTAG 59.830 55.000 9.92 0.00 38.10 2.57
110 119 0.944311 GAAGCTCGAAACGCTCCACA 60.944 55.000 0.00 0.00 36.56 4.17
122 131 4.397417 AGATGAAAAATCAAGGGAAGCTCG 59.603 41.667 0.00 0.00 0.00 5.03
201 210 6.096846 GCCCCAAGTGATTTCATAGTAAATGT 59.903 38.462 0.00 0.00 0.00 2.71
213 222 2.102578 GCACATAGCCCCAAGTGATTT 58.897 47.619 0.00 0.00 37.23 2.17
273 373 3.753815 TGACAAGTGCAAATCTGATGGA 58.246 40.909 0.00 0.00 0.00 3.41
291 391 5.233476 TGAAGAACGTGATACACACTTTGAC 59.767 40.000 0.00 0.00 46.24 3.18
294 394 5.113383 TGTGAAGAACGTGATACACACTTT 58.887 37.500 12.46 0.00 46.24 2.66
302 402 9.658475 CAAGTTTAATTTGTGAAGAACGTGATA 57.342 29.630 0.00 0.00 31.32 2.15
445 545 0.563672 ATCCAGTCCTCCCTACCCTC 59.436 60.000 0.00 0.00 0.00 4.30
447 547 0.563672 AGATCCAGTCCTCCCTACCC 59.436 60.000 0.00 0.00 0.00 3.69
451 551 2.293184 TGCTTAAGATCCAGTCCTCCCT 60.293 50.000 6.67 0.00 0.00 4.20
476 576 3.614150 GCTGTCGTTGATCAGTTCCACTA 60.614 47.826 0.00 0.00 34.57 2.74
506 606 8.684386 TTTGGACATCTACACATAAACAAAGA 57.316 30.769 0.00 0.00 0.00 2.52
518 618 5.316167 AGCACAGAATTTTGGACATCTACA 58.684 37.500 0.57 0.00 0.00 2.74
595 708 2.093235 AGTGGTGCCTCTGCTTATTCTC 60.093 50.000 0.00 0.00 38.71 2.87
653 767 1.275657 GTTCGTTGGCACAGTCACG 59.724 57.895 2.39 2.39 42.39 4.35
762 876 6.470456 ACATCAGATGGTATAGGAGTAGGA 57.530 41.667 15.13 0.00 33.60 2.94
763 877 7.546250 AAACATCAGATGGTATAGGAGTAGG 57.454 40.000 15.13 0.00 33.60 3.18
828 1261 8.926710 GTCTAATATGTATAATTGCAACGAGCT 58.073 33.333 0.00 0.00 45.94 4.09
928 1361 5.756833 GTGGTTTGTAGCCTATAATAACGCT 59.243 40.000 0.00 0.00 35.34 5.07
973 1406 1.615107 CGTTGGTCTCTTTCGGTCGC 61.615 60.000 0.00 0.00 0.00 5.19
1048 1481 1.000019 CGTGGAGAGGAGGGTGGTA 60.000 63.158 0.00 0.00 0.00 3.25
1156 1589 1.180456 TTGTAGTCCCAGAACGCCGA 61.180 55.000 0.00 0.00 0.00 5.54
1157 1590 1.012486 GTTGTAGTCCCAGAACGCCG 61.012 60.000 0.00 0.00 0.00 6.46
1380 1813 4.118995 TACCGTGCGGCGTAGTGG 62.119 66.667 9.37 11.79 39.32 4.00
1432 1869 1.222387 CCGCCAAATTCCCTCGGTA 59.778 57.895 0.00 0.00 35.75 4.02
1499 1941 1.203758 CTCCACGTACCTGCACATACA 59.796 52.381 0.00 0.00 0.00 2.29
1870 2312 2.029518 CAGCACGCACCACTGAGA 59.970 61.111 0.00 0.00 33.10 3.27
2086 2543 1.804748 CCGTAGAAAGTGAAGTTGGCC 59.195 52.381 0.00 0.00 0.00 5.36
2118 2575 1.555075 CGATTTGGTCTGAAGGGGAGA 59.445 52.381 0.00 0.00 0.00 3.71
2120 2577 0.618458 CCGATTTGGTCTGAAGGGGA 59.382 55.000 0.00 0.00 0.00 4.81
2121 2578 3.175133 CCGATTTGGTCTGAAGGGG 57.825 57.895 0.00 0.00 0.00 4.79
2151 2608 0.666577 GTGAGTGAGTGCGTGGGTAC 60.667 60.000 0.00 0.00 0.00 3.34
2153 2610 2.421739 GTGAGTGAGTGCGTGGGT 59.578 61.111 0.00 0.00 0.00 4.51
2154 2611 2.357517 GGTGAGTGAGTGCGTGGG 60.358 66.667 0.00 0.00 0.00 4.61
2155 2612 2.734723 CGGTGAGTGAGTGCGTGG 60.735 66.667 0.00 0.00 0.00 4.94
2156 2613 2.734723 CCGGTGAGTGAGTGCGTG 60.735 66.667 0.00 0.00 0.00 5.34
2157 2614 3.224324 ACCGGTGAGTGAGTGCGT 61.224 61.111 6.12 0.00 0.00 5.24
2158 2615 2.137425 TACACCGGTGAGTGAGTGCG 62.137 60.000 40.21 10.82 40.34 5.34
2159 2616 0.032952 TTACACCGGTGAGTGAGTGC 59.967 55.000 40.21 0.00 40.34 4.40
2160 2617 1.340248 AGTTACACCGGTGAGTGAGTG 59.660 52.381 40.21 12.51 40.34 3.51
2161 2618 1.700955 AGTTACACCGGTGAGTGAGT 58.299 50.000 40.21 19.60 40.34 3.41
2162 2619 2.035449 TGAAGTTACACCGGTGAGTGAG 59.965 50.000 40.21 14.10 40.34 3.51
2163 2620 2.033372 TGAAGTTACACCGGTGAGTGA 58.967 47.619 40.21 19.03 40.34 3.41
2164 2621 2.132762 GTGAAGTTACACCGGTGAGTG 58.867 52.381 40.21 15.41 43.65 3.51
2165 2622 2.037144 AGTGAAGTTACACCGGTGAGT 58.963 47.619 40.21 21.95 41.12 3.41
2166 2623 2.035449 TCAGTGAAGTTACACCGGTGAG 59.965 50.000 40.21 16.60 41.12 3.51
2167 2624 2.033372 TCAGTGAAGTTACACCGGTGA 58.967 47.619 40.21 21.04 41.12 4.02
2168 2625 2.519377 TCAGTGAAGTTACACCGGTG 57.481 50.000 32.83 32.83 41.12 4.94
2169 2626 2.289444 CCATCAGTGAAGTTACACCGGT 60.289 50.000 0.00 0.00 41.12 5.28
2170 2627 2.346803 CCATCAGTGAAGTTACACCGG 58.653 52.381 0.00 0.00 41.12 5.28
2171 2628 1.732259 GCCATCAGTGAAGTTACACCG 59.268 52.381 0.00 0.00 41.12 4.94
2172 2629 2.484264 GTGCCATCAGTGAAGTTACACC 59.516 50.000 0.00 0.00 41.12 4.16
2173 2630 2.157668 CGTGCCATCAGTGAAGTTACAC 59.842 50.000 0.00 0.40 40.60 2.90
2174 2631 2.412870 CGTGCCATCAGTGAAGTTACA 58.587 47.619 0.00 0.00 0.00 2.41
2175 2632 1.128692 GCGTGCCATCAGTGAAGTTAC 59.871 52.381 0.00 0.00 0.00 2.50
2176 2633 1.270571 TGCGTGCCATCAGTGAAGTTA 60.271 47.619 0.00 0.00 0.00 2.24
2177 2634 0.534877 TGCGTGCCATCAGTGAAGTT 60.535 50.000 0.00 0.00 0.00 2.66
2178 2635 0.952497 CTGCGTGCCATCAGTGAAGT 60.952 55.000 0.00 0.00 0.00 3.01
2179 2636 0.671472 TCTGCGTGCCATCAGTGAAG 60.671 55.000 0.00 0.00 0.00 3.02
2180 2637 0.671472 CTCTGCGTGCCATCAGTGAA 60.671 55.000 0.00 0.00 0.00 3.18
2191 2648 3.816920 CGCGTCGAACTCTGCGTG 61.817 66.667 0.00 0.47 45.12 5.34
2208 2669 4.666253 TGCACCAGCCTGAAGCCC 62.666 66.667 0.00 0.00 45.47 5.19
2352 2821 3.272334 GCGATCATGGGGTGCGTC 61.272 66.667 0.00 0.00 0.00 5.19
2651 3229 0.097325 CGCGCCCGCAATAGTAAAAA 59.903 50.000 13.42 0.00 42.06 1.94
2769 3358 3.670627 GCAGCATTTCCTTGGTCTTTACG 60.671 47.826 0.00 0.00 0.00 3.18
2844 3434 4.207019 CGAAACCTGCTGAAATTTGACAAC 59.793 41.667 0.00 0.00 0.00 3.32
2867 3458 5.934935 TCGAACAGGACTCAAATTTAACC 57.065 39.130 0.00 0.00 0.00 2.85
3146 3760 1.272490 GAGACATCGACCTTCACCACA 59.728 52.381 0.00 0.00 0.00 4.17
3191 3805 3.682292 GAACTTGCGCCCCTCGGAT 62.682 63.158 4.18 0.00 38.62 4.18
3292 3906 6.174720 AGAGTTTTGTATGAACTGACAGGA 57.825 37.500 7.51 0.00 37.46 3.86
3334 3954 6.405176 GCCTGGAATCTTTGGAAGTTATTGAG 60.405 42.308 0.00 0.00 0.00 3.02
3339 3959 3.244770 ACGCCTGGAATCTTTGGAAGTTA 60.245 43.478 0.00 0.00 0.00 2.24
3345 3965 1.885887 TGAAACGCCTGGAATCTTTGG 59.114 47.619 0.00 0.00 0.00 3.28
3359 3979 5.630264 TCAAATGATGCTGATGTTTGAAACG 59.370 36.000 3.37 0.00 36.27 3.60
3566 4186 1.593196 TTGCTTTTCAGAGTCGGTGG 58.407 50.000 0.00 0.00 0.00 4.61
3571 4191 4.791974 CCTGACAATTGCTTTTCAGAGTC 58.208 43.478 19.93 2.74 38.19 3.36
3579 4199 1.260544 GGGAGCCTGACAATTGCTTT 58.739 50.000 5.05 0.00 34.99 3.51
3597 4217 4.070630 TCAGATTTTTGCCCAGTTTTGG 57.929 40.909 0.00 0.00 44.60 3.28
3699 4319 2.223135 GCAAGATTTCGCAAGCTCCTAC 60.223 50.000 0.00 0.00 37.18 3.18
3710 4331 4.870221 TCATCAGTGATGCAAGATTTCG 57.130 40.909 25.53 1.19 39.63 3.46
3711 4332 5.338365 GGTTCATCAGTGATGCAAGATTTC 58.662 41.667 25.53 4.52 39.63 2.17
3777 4401 7.071069 TCCATAGTTCATATCAACTGCATCT 57.929 36.000 1.72 0.00 37.20 2.90
3894 4519 3.323979 ACAGTGTCCGTCTTAGTTTCCAT 59.676 43.478 0.00 0.00 0.00 3.41
3935 4560 4.517453 TCCTAGTGATTTCGTTTGGGTTTG 59.483 41.667 0.00 0.00 0.00 2.93
3943 4568 8.289939 TCAGTTATAGTCCTAGTGATTTCGTT 57.710 34.615 0.00 0.00 0.00 3.85
3987 4612 0.031585 TCGTCGACTTCACACTTGGG 59.968 55.000 14.70 0.00 0.00 4.12
4273 4898 0.618458 GTTGGGTGGATCTGCACCTA 59.382 55.000 18.67 11.43 41.07 3.08
4276 4901 2.418368 TATGTTGGGTGGATCTGCAC 57.582 50.000 0.00 0.00 0.00 4.57
4302 5009 0.104304 AGCTGTTCCGTCAAAGTCGT 59.896 50.000 0.00 0.00 0.00 4.34
4312 5019 5.048507 GGAGTACCTTATTTAGCTGTTCCG 58.951 45.833 0.00 0.00 0.00 4.30
4332 5039 6.054860 ACAATTAATATGGATCGGAGGGAG 57.945 41.667 0.00 0.00 0.00 4.30
4333 5040 5.337250 CGACAATTAATATGGATCGGAGGGA 60.337 44.000 0.00 0.00 0.00 4.20
4334 5041 4.870426 CGACAATTAATATGGATCGGAGGG 59.130 45.833 0.00 0.00 0.00 4.30
4335 5042 4.330074 GCGACAATTAATATGGATCGGAGG 59.670 45.833 0.00 0.00 0.00 4.30
4336 5043 5.062683 CAGCGACAATTAATATGGATCGGAG 59.937 44.000 0.00 0.00 0.00 4.63
4337 5044 4.929211 CAGCGACAATTAATATGGATCGGA 59.071 41.667 0.00 0.00 0.00 4.55
4338 5045 4.929211 TCAGCGACAATTAATATGGATCGG 59.071 41.667 0.00 0.00 0.00 4.18
4339 5046 6.653273 ATCAGCGACAATTAATATGGATCG 57.347 37.500 0.00 0.00 0.00 3.69
4340 5047 9.979270 CTAAATCAGCGACAATTAATATGGATC 57.021 33.333 0.00 0.00 0.00 3.36
4341 5048 9.507329 ACTAAATCAGCGACAATTAATATGGAT 57.493 29.630 0.00 0.00 0.00 3.41
4342 5049 8.902540 ACTAAATCAGCGACAATTAATATGGA 57.097 30.769 0.00 0.00 0.00 3.41
4347 5054 9.162764 AGTTGTACTAAATCAGCGACAATTAAT 57.837 29.630 0.00 0.00 36.39 1.40
4348 5055 8.542497 AGTTGTACTAAATCAGCGACAATTAA 57.458 30.769 0.00 0.00 36.39 1.40
4349 5056 8.542497 AAGTTGTACTAAATCAGCGACAATTA 57.458 30.769 0.00 0.00 36.39 1.40
4350 5057 7.435068 AAGTTGTACTAAATCAGCGACAATT 57.565 32.000 0.00 0.00 36.39 2.32
4351 5058 7.041372 ACAAAGTTGTACTAAATCAGCGACAAT 60.041 33.333 0.00 0.00 40.16 2.71
4352 5059 6.259167 ACAAAGTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
4353 5060 5.756347 ACAAAGTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
4354 5061 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
4355 5062 7.949903 TTACAAAGTTGTACTAAATCAGCGA 57.050 32.000 3.38 0.00 42.84 4.93
4356 5063 9.607285 AAATTACAAAGTTGTACTAAATCAGCG 57.393 29.630 3.38 0.00 42.84 5.18
4370 5077 9.607285 CGCTGATTTAGTACAAATTACAAAGTT 57.393 29.630 0.00 0.00 0.00 2.66
4371 5078 8.780249 ACGCTGATTTAGTACAAATTACAAAGT 58.220 29.630 0.00 0.00 0.00 2.66
4372 5079 9.262472 GACGCTGATTTAGTACAAATTACAAAG 57.738 33.333 0.00 0.00 0.00 2.77
4373 5080 8.775527 TGACGCTGATTTAGTACAAATTACAAA 58.224 29.630 0.00 0.00 0.00 2.83
4374 5081 8.312896 TGACGCTGATTTAGTACAAATTACAA 57.687 30.769 0.00 0.00 0.00 2.41
4375 5082 7.892778 TGACGCTGATTTAGTACAAATTACA 57.107 32.000 0.00 0.00 0.00 2.41
4376 5083 9.769093 AATTGACGCTGATTTAGTACAAATTAC 57.231 29.630 0.00 0.00 0.00 1.89
4397 5104 5.785423 ACTCCCTCCGATCCATATTAATTGA 59.215 40.000 0.00 0.00 0.00 2.57
4424 5131 4.576873 TGCCGTCAAACTTTATCAACTTCA 59.423 37.500 0.00 0.00 0.00 3.02
4431 5138 6.417191 TGATAGTTGCCGTCAAACTTTATC 57.583 37.500 0.70 0.91 33.37 1.75
4437 5144 4.226761 CCTTTTGATAGTTGCCGTCAAAC 58.773 43.478 0.00 0.00 40.42 2.93
4445 5152 9.508567 GATGAAAGATAACCTTTTGATAGTTGC 57.491 33.333 0.00 0.00 44.63 4.17


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.